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Journal of Bacteriology, March 2007, p. 1931-1945, Vol. 189, No. 5
0021-9193/07/$08.00+0     doi:10.1128/JB.01259-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Whole-Genome Analysis of the Methyl tert-Butyl Ether-Degrading Beta-Proteobacterium Methylibium petroleiphilum PM1 ^,

Staci R. Kane,^1,* Anu Y. Chakicherla,^1, Patrick S. G. Chain,^1,4 Radomir Schmidt,² Maria W. Shin,¹ Tina C. Legler,¹ Kate M. Scow,² Frank W. Larimer,^3,4 Susan M. Lucas,⁴ Paul M. Richardson,⁴ and Krassimira R. Hristova²

Lawrence Livermore National Laboratory, Livermore, California,¹ Department of Land Air and Water Resources, University of California, Davis, California,² Genome Analysis Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee,³ Joint Genome Institute Production Genomics Facility, Walnut Creek, California⁴

Received 10 August 2006/ Accepted 29 November 2006

Methylibium petroleiphilum PM1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (MTBE). Strain PM1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (C₅ to C₁₂) hydrocarbons present in petroleum products. Whole-genome analysis of PM1 revealed an 4-Mb circular chromosome and an 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. Aromatic hydrocarbon and alkane degradation, metal resistance, and methylotrophy are encoded on the chromosome. The megaplasmid contains an unusual t-RNA island, numerous insertion sequences, and large repeated elements, including a 40-kb region also present on the chromosome and a 29-kb tandem repeat encoding phosphonate transport and cobalamin biosynthesis. The megaplasmid also codes for alkane degradation and was shown to play an essential role in MTBE degradation through plasmid-curing experiments. Discrepancies between the insertion sequence element distribution patterns, the distributions of best BLASTP hits among major phylogenetic groups, and the G+C contents of the chromosome (69.2%) and plasmid (66%), together with comparative genome hybridization experiments, suggest that the plasmid was recently acquired and apparently carries the genetic information responsible for PM1's ability to degrade MTBE. Comparative genomic hybridization analysis with two PM1-like MTBE-degrading environmental isolates (99% identical 16S rRNA gene sequences) showed that the plasmid was highly conserved (ca. 99% identical), whereas the chromosomes were too diverse to conduct resequencing analysis. PM1's genome sequence provides a foundation for investigating MTBE biodegradation and exploring the genetic regulation of multiple biodegradation pathways in M. petroleiphilum and other MTBE-degrading beta-proteobacteria.

Published ahead of print on 8 December 2006.

Supplemental material for this article may be found at http://jb.asm.org/.

S.R.K. and A.Y.C. gave equal contributions to this study.

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